scholarly journals Facing the Environment: Small RNAs and the Regulation of Gene Expression Under Abiotic Stress in Plants

10.5772/22250 ◽  
2011 ◽  
Author(s):  
Ines Trindade ◽  
Dulce Santos ◽  
Tamas Dalmay ◽  
Pedro Fevereiro
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Small Rnas ◽  
Regulation Of Gene Expression

scholarly journals Using pan RNA-seq analysis to reveal the ubiquitous existence of 5’ end and 3’ end small RNAs

2018 ◽  
Author(s):  
Xiaofeng Xu ◽  
Haishuo Ji ◽  
Zhi Cheng ◽  
Xiufeng Jin ◽  
Xue Yao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Steady State ◽  
Small Rnas ◽  
Gene Expression Regulation ◽  
Regulation Of Gene Expression ◽  
Cost Effective ◽  
Rna Degradation ◽  
Point Of View ◽  
Rna Seq ◽  
Dsrna Cleavage

AbstractIn this study, we used pan RNA-seq analysis to reveal the ubiquitous existence of 5’ end and 3’ end small RNAs. 5’ and 3’ sRNAs alone can be used to annotate mitochondrial with 1-bp resolution and nuclear non-coding genes and identify new steady-state RNAs, which are usually from functional genes. Using 5’, 3’ and intronic sRNAs, we revealed that the enzymatic dsRNA cleavage and RNAi could involve in the RNA degradation and gene expression regulation of U1 snRNA in human. The further study of 5’, 3’ and intronic sRNAs help rediscover double-stranded RNA (dsRNA) cleavage, RNA interference (RNAi) and the regulation of gene expression, which challenges the classical theories. In this study, we provided a simple and cost effective way for the annotation of mitochondrial and nuclear non-coding genes and the identification of new steady-state RNAs, particularly long non-coding RNAs (lncRNAs). We also provided a different point of view for cancer and virus, based on the new discoveries of dsRNA cleavage, RNAi and the regulation of gene expression.

scholarly journals Post-transcriptional Regulation of Gene Expression in Plants during Abiotic Stress

2009 ◽  
Vol 10 (7) ◽  
pp. 3168-3185 ◽  
Author(s):  
Maïna Floris ◽  
Hany Mahgoub ◽  
Elodie Lanet ◽  
Christophe Robaglia ◽  
Benoît Menand
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Abiotic Stress ◽  
Regulation Of Gene Expression ◽  
Post Transcriptional Regulation

scholarly journals miR-155 Inhibits Expression of the MEF2A Protein to Repress Skeletal Muscle Differentiation

2011 ◽  
Vol 286 (41) ◽  
pp. 35339-35346 ◽  
Author(s):  
Hee Young Seok ◽  
Mariko Tatsuguchi ◽  
Thomas E. Callis ◽  
Aibin He ◽  
William T. Pu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Myogenic Differentiation ◽  
Regulation Of Gene Expression ◽  
Myoblast Differentiation ◽  
Transcriptional Level ◽  
Muscle Gene Expression ◽  
Important Regulator ◽  
Non Coding Rnas ◽  
Muscle Gene

microRNAs (miRNAs) are 21–23-nucleotide non-coding RNAs. It has become more and more evident that this class of small RNAs plays critical roles in the regulation of gene expression at the post-transcriptional level. MEF2A is a member of the MEF2 (myogenic enhancer factor 2) family of transcription factors. Prior report showed that the 3′-untranslated region (3′-UTR) of the Mef2A gene mediated its repression; however, the molecular mechanism underlying this intriguing observation was unknown. Here, we report that MEF2A is repressed by miRNAs. We identify miR-155 as one of the primary miRNAs that significantly represses the expression of MEF2A. We show that knockdown of the Mef2A gene by siRNA impairs myoblast differentiation. Similarly, overexpression of miR-155 leads to the repression of endogenous MEF2A expression and the inhibition of myoblast differentiation. Most importantly, reintroduction of MEF2A in miR-155 overexpressed myoblasts was able to partially rescue the miR-155-induced myoblast differentiation defect. Our data therefore establish miR-155 as an important regulator of MEF2A expression and uncover its function in muscle gene expression and myogenic differentiation.

scholarly journals Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic

2021 ◽  
Author(s):  
Kyung Moon ◽  
Minji Sim ◽  
Chin-Hsien Tai ◽  
Kyungyoon Yoo ◽  
Charlotte Merzbacher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Posttranscriptional Regulation ◽  
Transcriptome Sequencing ◽  
Regulation Of Gene Expression ◽  
Bacterial Virulence ◽  
Human Pathogen ◽  
Rna Seq ◽  
Content Type ◽  
Search Program

Noncoding small RNAs (sRNAs) are crucial for posttranscriptional regulation of gene expression in all organisms and are known to be involved in the regulation of bacterial virulence. We have investigated the presence of sRNAs in the obligate human pathogen B. pertussis , using transcriptome sequencing (RNA-seq) and the recently developed prokaryotic sRNA search program ANNOgesic.

scholarly journals Sub-cellular mRNA localization modulates the regulation of gene expression by small RNAs in bacteria

2017 ◽  
Vol 14 (5) ◽  
pp. 056001 ◽  
Author(s):  
Hamid Teimouri ◽  
Elgin Korkmazhan ◽  
Joel Stavans ◽  
Erel Levine
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Regulation Of Gene Expression ◽  
Mrna Localization

scholarly journals Direct and Indirect Transcriptional Effects of Abiotic Stress in Zea mays Plants Defective in RNA-Directed DNA Methylation

2021 ◽  
Vol 12 ◽  
Author(s):  
Thelma F. Madzima ◽  
Stefania Vendramin ◽  
Jason S. Lynn ◽  
Phebe Lemert ◽  
Katherine C. Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zea Mays ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Water Deprivation ◽  
Regulation Of Gene Expression ◽  
Differentially Expressed ◽  
Dependent Manner ◽  
Transcriptional Responses

Plants respond to abiotic stress stimuli, such as water deprivation, through a hierarchical cascade that includes detection and signaling to mediate transcriptional and physiological changes. The phytohormone abscisic acid (ABA) is well-characterized for its regulatory role in these processes in response to specific environmental cues. ABA-mediated changes in gene expression have been demonstrated to be temporally-dependent, however, the genome-wide timing of these responses are not well-characterized in the agronomically important crop plant Zea mays (maize). ABA-mediated responses are synergistic with other regulatory mechanisms, including the plant-specific RNA-directed DNA methylation (RdDM) epigenetic pathway. Our prior work demonstrated that after relatively long-term ABA induction (8 h), maize plants homozygous for the mop1-1 mutation, defective in a component of the RdDM pathway, exhibit enhanced transcriptional sensitivity to the phytohormone. At this time-point, many hierarchically positioned transcription factors are differentially expressed resulting in primary (direct) and secondary (indirect) transcriptional outcomes. To identify more immediate and direct MOP1-dependent responses to ABA, we conducted a transcriptomic analysis using mop1-1 mutant and wild type plants treated with ABA for 1 h. One h of ABA treatment was sufficient to induce unique categories of differentially expressed genes (DEGs) in mop1-1. A comparative analysis between the two time-points revealed that distinct epigenetically-regulated changes in gene expression occur within the early stages of ABA induction, and that these changes are predicted to influence less immediate, indirect transcriptional responses. Homology with MOP1-dependent siRNAs and a gene regulatory network (GRN) were used to identify putative immediate and indirect targets, respectively. By manipulating two key regulatory networks in a temporal dependent manner, we identified genes and biological processes regulated by RdDM and ABA-mediated stress responses. Consistent with mis-regulation of gene expression, mop1-1 homozygous plants are compromised in their ability to recover from water deprivation. Collectively, these results indicate transcriptionally and physiologically relevant roles for MOP1-mediated regulation of gene expression of plant responses to environmental stress.

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